Background
The Norwegian Veterinary Institute (NVI) sequences a lot of pathogenic bacteria, bacteria that can cause disease. This is done both for various research projects, but also to monitor how different pathogens move and behave in a Norwegian context. A majority of the pathogens that NVI focus on are foodborne bacteria that affect humans, like Salmonella, E. coli and Listeria. These can cause serious illness, and in some cases death. Finding out more about the properties of these pathogens, how they evolve and where they come from can help combat disease.
Thesis
The aim of this project is to apply various machine learning methods to explore the properties of pathogens and to see how they behave. Different aspects of pathogen behavior can be explored, such as how pathogens become resistant to antibiotics, which genetic factors that contribute to their pathogenicity, and which food sources they come from. The focus of the thesis will be decided upon in collaboration with the student. This work will entail managing and analyzing large datasets, learning and using several different machine learning libraries, and working in a high performance computing setting.
The candidate
The student that takes on this project should have a background in computer science or informatics, and have an interest in biology and bioinformatics. The student should have good programming skills in at least one language, and be willing to learn R or python. The student should also be familiar with the Linux command line. The student will collaborate with researchers from the Dept. of Informatics and Dept. of Pharmacy at the University of Oslo, and the NVI. The student would also be expected to visit the Veterinary Institute in Ås as the project requires.
Contact
If you find this interesting and would like to know more, feel free to contact Karin Lagesen. Depending on the applicants, multiple different projects might be created.